I have a WordPress multisite network with the first site in the network: netmix.co

Additional sites are:

netmix.com
digitalstrategyworks.com

All my content is there, but all theme images and CSS and thumbnails on the site and in my admin are now unavailable. I'm thinking this is a server/permissions issue and I just can't figure out how to solve it.

I have an .htaccess file in the wp-content folder, but I disabled it and that didn't help.
I turned off all plugins and swapped a theme like Twenty-Twelve, and all theme images were still broken.

I do have plugins like WP Security Scan and Sucuri and tried to harden WordPress and I think this is when this started to happen. The only way to bring everything back is to go to an older backup and restore.

Checked all folder permissions for wp-content, themes and theme folders and they are 755.

I also set all permissions: directories to 755 and files to 644 to ensure that the primary directory permissions are correct.

I am running on Linode and recently updated all my LInode packages. I do believe I have NGINX running, but it's not necessarily configured at the moment for WordPress, because I'm a noobie at this and someone installed it, but hasn't configured it and I'm afraid to configure it because "wordpress" is not my root directory on some sites, since I changed the name of the root directory to something else to harden WordPress and many of the tutorials look like the reference a root folder name of WordPress.

It's been 5-days since your reply, so what I did was restore to an earlier version on June 26th and that restored everything.

There were two events that happened.

First, I updated Plesk to the latest version, which has new WordPress controls for Plesk administrators.

Second, I upgraded about 28 packages on the web server that needed to be updated.

Something in all that may have been a problem, so I reverted back to the earlier backup. In that, we lost some changes and emails, but such is life.

I had a sys admin and a Plesk support person look into all of this but no one could figure out the permissions changes and issues that arose and even after resetting permissions things didn't work. Just a big mess.

It's all fixed now though, but lost some things, which is why it's so important to backup before you do any of this.

- All theme thumbnails are missing under Themes folder
- When activate any other theme, all style break for that theme, especially in Netmix.com.
- All admin panels for plugins and themes have lost their CSS, but all functionality is still available; ex. I can see all text for JetPack, but all the style disappeared.

Steps taken to try and fix:

1. Disabled all plugins and reset plugins from FTP, did not fix issue
2. Reinstalled 3.9.1 through admin panel to see if that is the issue, did not fix issue
3. Manually uploaded new wp-admin, wp-includes folders, did not fix issue

This is only happening for every site in the network.

I've contacted Plesk and they say there is no issue on their end, because the multisite is not connected to their new WordPress management system.